... tweaked styling of several functional tests (the non-toolbox,datamanager,workflow,api functional tests) along the way - mostly PEP-8 fixes and eliminating * imports. Did not modify tests which do not pass - but did not in the source where they fail inside a TODO.
Include the automatic creation of a new DatasetPermission for an hda where the DATASET_MANAGE_PERMISSION permission is associated with the hda.history.user's private role if the hda has no roles associated with the DATASET_MANAGE_PERMISSION permission. The creation of the DatasetPermission occurs when the user clicks the pencil icon for the hda.
1. Fix a bug that included the option for a regular user to upload a directory of files when the config setting existed, but the user's directory did not exist.  Instead of throwing an exception, an attempt to create the directory will now be done.  If the attempt fails, the option to "Upload a directory of files" will not be included in the select list on the upload form.
2. When browsing a data library, only display the check boxes and the actions to perform on multiple selected datasets if library datasets are displayed.
3. Clean up the behavior when performing an action on multiple library datasets.  Instead of throwing an error and not allowing the action on any of the datasets if the user is not authorized to perform the action on 1 of them, all "unauthorized" datasets are now left alone and the action is performed on all datasets for which the user is authorized to perform the action.  Appropriate messages detail what occurred.
4. Allow regular users to delete multiple datasets returned from library dataset searches based on the behavior described in 3 above.
5. Do not include the "Select datasets for import into selected histories" option in the actions pop-up menu at the data library level if the library's root folder doesn't contain any accessible datasets.  Make behavior the same for folder popup menus.
6.  Add a new LibraryFolder.active_datasets mapper and eliminate the incorrect LibraryFolder.active_library_datasets property.  Callers of the incorrect property now use the mapper.
7. Eliminate the incorrect LibraryFolder.active_datasets property.
8. Fix the queries in the library_common controller's active_folders_and_lddas() and activable_folders_and_lddas() methods to return library_datasets instead of lddas, and rename the methods to be active_folders_and_library_datasets(0 and activatable_folders_and_library_datasets() respectively.
9. Fix bug where regular user could never see deleted library items when toggling show / hide deleted items.
10. Fix functional test for uploading directories of files to a library folder.  The test generally failed because not enough time would elapse before checking if the files uploaded.  The check is now performed in a later method in the test script, hopefully allowing for enough time to pass.
11. Functional test code clarifications for the browse_library() test method.
1. Enhance importing library dataset into the current history by now allowing the user to select from a list of existing histories or create a new named history ( similar to copying datasets ).  This feature is available for a specific library dataset, a folder ( or root folder ), when selecting multiple datasets from in a library,  and on the results page for searched library datasets.
2. Add Brad Chapman's latest patch for fixing the lucene search implementation
3. Eliminate searches on dataset state for both whoosh and lucene searches
4. Clarify the objects being searched in the regular search and advanced search boxes in the data libraries grids.
5. Add the ability to perform certain actions on 1 or more selected library datasets on the results page for searched library datasets.
6. Add a "select all" checkbox to the browse_library.mako template.
7. Fixed library functional tests accordingly.
(2) Enhance and cleanup the test_library_security.py functional test script to cover new features.
(3) Clean up security checking code recently added to the library-common controller by creating methods for checking permissions and calling the methods when necessary.
(4) Add checks to the security controller methods to only flush to the db when necessary.
(5) Add a pop-up menu for folders in the Data Libraries perspective to enable users to view folder information since it may include template information.
(6) Fix all currently broken library-related functional test - should now all be green.
John Chilton